The real problem/fault is that the codes come in a frame and that the codes themselves have some sort of margin included/embeded. I'm guessing this is the safety margin for the codes to be readable, but as a result it is impossible to accurately (re)size and/or align them, and I would honestly see no reason why ID could not have a setting to override that.
QR codes were added some time ago and I don't think they were ever really improved upon.
Report bugs or make a feature request
https://indesign.uservoice.com/
I do recommend Barcode Studio though.
But there are plenty of QR code generators out there for free that might be better.
As mentioned they are just in graphic frames
In the file I sent you
Go to Window>Styles>Object Styles
You'll see the QR ObjectStyle I created
And increase the crop amount

This gets it close to the edge of the frame.
It's not perfect. But I assume as you do it's to do with a hidden setting for a quiet zone for the barcode.
If it's that important then I really think you should find a QR generator that can do what you need.